Download MendeleyCrystal structure of the DNA decamer d(CGCAATTGCG) complexed with the minor groove binding drug netropsin.
Nunn, C.M., Garman, E., Neidle, S.(1997) Biochemistry 36: 4792-4799
- PubMed: 9125500
- DOI: https://doi.org/10.1021/bi9628228
- Primary Citation of Related Structures:
261D - PubMed Abstract:
The crystal structure of netropsin bound to the decamer d(CGCAATTGCG) has been determined at 2.4 A resolution. This is the first example of a crystal structure of netropsin bound to decamer DNA. The central eight bases of each DNA single-strand base pair with a self-complementary strand to form an octamer B-DNA duplex. These duplexes lie end to end within the unit cell. The terminal 5'-C and G-3' bases are unpaired and interact with the neighboring duplexes via interactions within both the major and minor groove to form base triplet interactions of the type C(+)-G x C and G*(G x C), respectively. The triplet interaction of the type C(+)-G x C is known to exist within triplex DNA with the C+ base oriented parallel with the Watson-Crick guanine base to which it hydrogen bonds. The netropsin molecule lies within the minor groove of the octamer duplex and assumes a class I type position, with bifurcated hydrogen-bonding interactions from the amide groups of the netropsin to the A x T base pairs of the minor groove. The netropsin molecule fits within a five base pair long minor groove site by bending of the flexible amidinium group at one end of the drug.
Organizational Affiliation:
The CRC Biomolecular Structure Unit, The Institute of Cancer Research, Sutton, Surrey, U.K. c.nunn@icr.ac.uk
